Mercurial > repos > iuc > art
changeset 4:531ff1d417b6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
| author | iuc |
|---|---|
| date | Fri, 07 Sep 2018 10:57:50 -0400 |
| parents | bb7e0ccc0029 |
| children | ff8599e52a55 |
| files | art_solid.xml macros.xml tool_dependencies.xml |
| diffstat | 3 files changed, 39 insertions(+), 44 deletions(-) [+] |
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--- a/art_solid.xml Tue Jun 28 11:32:19 2016 -0400 +++ b/art_solid.xml Fri Sep 07 10:57:50 2018 -0400 @@ -8,51 +8,52 @@ <command><![CDATA[ art_SOLiD -$sam + $sam -#if $rndSeed and $rndSeed > -1: - -r $rndSeed -#end if + #if $rndSeed and $rndSeed > -1: + -r $rndSeed + #end if + + #if $generate.amplicon.use_amplicon == "amplicon_true": + -A -#if $generate.amplicon.use_amplicon == "amplicon_true": - -A + #if $generate.choice == "single_end": + s + #else if $generate.choice == "paired_end": + p + #else: + m + #end if - #if $generate.choice == "single_end": - s - #else if $generate.choice == "paired_end": - p - #else: - m #end if -#end if - -$input_seq_file -output + '$input_seq_file' + output -#if $generate.choice == "single_end": - $generate.LEN_READ - $fold_coverage -#else if $generate.choice == "paired_end": - $generate.LEN_READ_F3 - $generate.LEN_READ_F5 - $fold_coverage - $generate.fragment_size - $generate.fragment_sd -#else: - $generate.LEN_READ - $fold_coverage - $generate.fragment_size - $generate.fragment_sd -#end if + #if $generate.choice == "single_end": + $generate.LEN_READ + $fold_coverage + #else if $generate.choice == "paired_end": + $generate.LEN_READ_F3 + $generate.LEN_READ_F5 + $fold_coverage + $generate.fragment_size + $generate.fragment_sd + #else: + $generate.LEN_READ + $fold_coverage + $generate.fragment_size + $generate.fragment_sd + #end if -#if $generate.amplicon.use_amplicon == "amplicon_true": - #if $generate.choice == "single_end": - $generate.amplicon.reads_per_amplicon - #else: - $generate.amplicon.read_pairs_per_amplicon + #if $generate.amplicon.use_amplicon == "amplicon_true": + #if $generate.choice == "single_end": + $generate.amplicon.reads_per_amplicon + #else: + $generate.amplicon.read_pairs_per_amplicon + #end if #end if -#end if + ]]></command> <inputs> <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/>
--- a/macros.xml Tue Jun 28 11:32:19 2016 -0400 +++ b/macros.xml Fri Sep 07 10:57:50 2018 -0400 @@ -63,7 +63,7 @@ <xml name="frag_len_sd"> <param label="the average DNA fragment size" - name="fragment_size" type="integer" value="200" minimum="101" /> + name="fragment_size" type="integer" value="200" /> <param label="the standard deviation of the DNA fragment size" name="fragment_sd" type="integer" value="0"/> </xml>
--- a/tool_dependencies.xml Tue Jun 28 11:32:19 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="art" version="2014_11_03"> - <repository changeset_revision="eaadf9edc5c1" name="package_art_2014_11_03" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>